[biomart-users] Error when searching across tables v0.9

[biomart-users] Error when searching across tables v0.9

Hello Arek/Others,

I've been trying to migrate to Biomart v0.9 from v0.7, but I am having trouble with some types of searches. I am uncertain if this is an issue with my setup or a bug. In my DB I have two tables joined by a common field (one to one). Nearly the same setup as v0.7. I can filter and browse the results fine except for instances where the filter is on a field in one table, but the requested attributes are on the other.

For example, the attached image shows a query that is failing. "Cage peaks" and "Annotation" are two separate tables joined by a `name_key`. If I don't try to filter on any "Annotation" field the query returns results. If I include any "Annotation" attribute in the query I get results. However, if I filter on an "Annotation" field but don't include an "Annotation" attribute BioMart shows "Error has occurred". For some reason the reverse, filter on the "CAGE Peak" field but don't include a "CAGE Peak" attribute, works fine.

The SQL log shows the following query is being run when the error occurs.

Re: [biomart-users] Error when searching across tables v0.9

Hi Jason,

The 'difficulty' that you are describing i.e filtering on one table and getting attributes from another should not be an issue. It is difficult for me to advise you any more on this without looking at your database schema.

One thing however that jumps at me looking at your incomplete query is that you are asking for the same attribute twice?

Anyway, i am happy to have a closer look if you send me the your schema dump

I've been trying to migrate to Biomart v0.9 from v0.7, but I am having trouble with some types of searches. I am uncertain if this is an issue with my setup or a bug. In my DB I have two tables joined by a common field (one to one). Nearly the same setup as v0.7. I can filter and browse the results fine except for instances where the filter is on a field in one table, but the requested attributes are on the other.

For example, the attached image shows a query that is failing. "Cage peaks" and "Annotation" are two separate tables joined by a `name_key`. If I don't try to filter on any "Annotation" field the query returns results. If I include any "Annotation" attribute in the query I get results. However, if I filter on an "Annotation" field but don't include an "Annotation" attribute BioMart shows "Error has occurred". For some reason the reverse, filter on the "CAGE Peak" field but don't include a "CAGE Peak" attribute, works fine.

The SQL log shows the following query is being run when the error occurs.